Understanding the response of soil quality indicators to changes in management practices is essential for sustainable land management. Soil quality indicators were measured for 2 years under established experiments with varying management histories and durations at four locations in New York State. The Willsboro (clay loam) and Aurora (silt loam) experiments were established in 1992, comparing no-till (NT) to plow-till (PT) management under corn (Zea mays L.)–soybean (Glycine max L.) rotation. The Chazy (silt loam) trial was established in 1973 as a factorial experiment comparing NT versus PT and the crop harvesting method (corn silage versus corn grain). The Geneva (silt loam) experiment was established in 2003 with vegetable rotations with and without intervening soil building crops, each under three tillage methods (NT, PT and zone-till (ZT)) and three cover cropping systems (none, rye and vetch). Physical indicators measured were wet aggregate stability (WAS), available water capacity (AWC) and surface hardness (SH) and subsurface hardness (SSH). Soil biological indicators included organic matter (OM), active carbon (AC), potentially mineralizable nitrogen (PMN) and root disease potential (RDP). Chemical indicators included pH, P, K, Mg, Fe, Mn and Zn. Results from the Willsboro and Aurora sites showed significant tillage effects for several indicators including WAS, AWC, OM, AC, pH, P, K, Mg, Fe and Mn. Generally, the NT treatment had better indicator values than the PT treatments. At the Chazy site, WAS, AWC, OM, AC, pH, K and Mg showed significant differences for tillage and/or harvest method, also with NT showing better indicator values compared to PT and corn grain better than corn silage. Aggregate stability was on average 2.5 times higher in NT compared to PT treatments at Willsboro, Aurora and Chazy sites. OM was also 1.2, 1.1 and 1.5 times higher in NT compared to PT treatments at Willsboro, Aurora and Chazy sites, respectively. At the Geneva site WAS, SH, AC, PMN, pH, P, K and Zn showed significant tillage effects. The cover crop effect was only significant for SH and PMN measurements. Indicators that gave consistent performance across locations included WAS, OM and AC, while PMN and RDP were site and management dependent. The composite soil health index (CSHI) significantly differentiated between contrasting management practices. The CSHI for the Willsboro site was 71% for NT and 59% for PT, while at the Aurora site it was 61% for NT and 48% for PT after 15 years of tillage treatments.